Is there a pipeline to determine the distance of a particle/vesicle from the nuclear edge? What is the best method to calculate this distance?
I suspect not, though it’s not an uncommon wish!
There are some finagling things you can do, though. Are your particles inside the nucleus? If so, you could:
1- Identify vesicles with IdentifyPrimary
2- Shrink those objects to their central point, using ExpandOrShrink
3- Identify nuclei with IdentifyPrimary
4- Perform a distance transform on the binary result of step 3 (not sure which module!)
5- MeasureObjectIntensity, measure the intensity of the image resulting from step 4, within each of the points from step 2. The intensity in each dot will be the distance from the edge.
The big caveat is I’m not sure which module to use for step 4, maybe someone can help on that! If your particles are in the cytoplasm, I’m not sure how to flip the distance transform in the other direction, or if we have a function for something like that.
If you want particles that are already inside the nucleus, that’s easy- RelateObjects will do that by selecting the option to calculate the distance to the parent’s edge, so all you need to do is identify both sets of objects and then use Relate. For something that’s not in the nucleus, that’s harder- you’d want to do something similar to what Anne laid out (distance transforms are in the Morph module), but I can’t think of any way to ensure that a vesicle in CellA that’s close to the nucleus in CellB wouldn’t get measured to the edge of NucleusB, not NucleusA. I’ll think about it more.